Long-chain (35–40 carbons) alkenones are a unique class of lipids biosynthesized by certain species of algae including the industrially grown marine microalgae Isochrysis. Their structures are characterized by a very long linear carbon-chain with trans double bonds and a methyl or ethyl ketone. A method is presented for the isolation of pure alkenones from Isochrysis biomass in parallel with biodiesel production. Yields for the isolated alkenones and biodiesel relative to the starting dry Isochrysis biomass were routinely 3.5 and 12% (w/w), respectively. Alkenones were then converted to smaller hydrocarbon fragments (jet-fuel range) by cross-metathesis with 2-butene (butenolysis) using several commercial ruthenium-based metathesis initiators. Butenolysis with the second-generation Hoveyda-Grubbs catalyst occurred rapidly at 4 °C, yielding near quantitative conversion within 30 min to a mixture containing mostly 8-decen-2-one (C10), 2,9-undecadiene (C12), and 2-heptadecene (C17) as both cis- and trans isomers based on analysis by comprehensive two-dimensional gas chromatography.